Habitat complexes exhibit varying vulnerability to human land use and thus have different impacts on biodiversity. In this study, we analyzed the effect of moderate land use on the plant species diversity in six characteristic Pannonian habitat complexes: forest steppe complex on sand, on dolomite, and on loess, as well as alkaline habitat complex, freshwater marsh complex, and zonal broadleaf colline forest. We chose two regions for each complex, and in each region, we selected a 2 x 2 km "natural" study site in a mostly protected area, and a moderately used "managed" site of the same size. We compared the alpha, beta, and gamma diversities of the total and the specialist species pools of the natural-managed site pairs by applying stratified random sampling and novel bootstrap statistics.The gamma diversity of the specialist species pool was found to be the most sensitive indicator of naturalness. It was higher in the natural sites of the loess and dolomite forest steppe and the freshwater marshland complexes, while there were no significant diversity differences in the other complexes. The diversity comparisons showed a consistent pattern: there were either no significant diversity differences in any of the natural-managed pairs, or there were significant differences in the gamma diversities of the specialist species pool in both the natural-managed pairs. We concluded that the same differences in naturalness may represent different sensitivities to human management as characterized by differences in diversity measures. Three habitat complexes, the loess and dolomite forest steppe and the freshwater marshland, require more focused nature protection efforts in order to preserve the habitat diversity, especially in maintaining the remnants of the natural woody patches and the most inundated habitats of the marshlands. In the case of the other studied complexes, moderate human land use can be harmonized by nature protection goals.